Biochemical and Biophysical Research Communications
GPS: a novel group-based phosphorylation predicting and scoring method
Section snippets
Methods
Data collection. We get the data set of phosphorylation sites from Phospho.ELM [24] which also includes the data of PhosphoBase [25]. After removing the phosphorylation sites with ambiguous information of PKs, we get 1404 items. We also manually checked the recent publications and got 597 more items. After clustering some homology PKs with too few known phosphorylation sites into a unique group, we got 52 PK families/PK groups, including ABL, ALK, AMPK, ATM, AURORA-B, BTK, CAK, CAM-II, CDK,
Performance on kinase PKA
We try to evaluate the performance of GPS method against two popular phosphorylation prediction systems, ScanSite 2.0 [20] and PredPhospho [21]. ScanSite 2.0 provides phosphorylation site prediction for 26 kinases, while PredPhospho only provides such functionality for four groups and four families of kinases. Besides most of the kinases in the above two systems, GPS method also includes several kinases which came into focus recently, e.g., Aurora-B. In the following, we will mainly evaluate
Acknowledgments
We thank Dr. T.J. Gibson and Dr. F. Diella for providing the data set of Phospho.ELM for this study. This work was supported by grants from Chinese Natural Science Foundation (39925018 and 30121001), Chinese Academy of Science (KSCX2-2-01), Chinese 973 project (2002CB713700), and American Cancer Society (RPG-99-173-01) to X. Yao. X. Yao is a GCC Distinguished Cancer Research Scholar.
References (38)
- et al.
NEK2A interacts with MAD1 and possibly functions as a novel integrator of the spindle checkpoint signaling
J. Biol. Chem.
(2004) - et al.
Role of Stat5 in type I interferon-signaling and transcriptional regulation
Biochem. Biophys. Res. Commun.
(2003) - et al.
Translational initiation regulators are hypophosphorylated in rat liver during ethionine-mediated ATP depletion
Biochem. Biophys. Res. Commun.
(2002) - et al.
Amino acid signalling and the integration of metabolism
Biochem. Biophys. Res. Commun.
(2004) - et al.
Extracellular calcium induces COX-2 in osteoblasts via a PKA pathway
Biochem. Biophys. Res. Commun.
(2004) - et al.
A role for hippocampal Rho-ROCK pathway in long-term spatial memory
Biochem. Biophys. Res. Commun.
(2004) - et al.
Target specificity analysis of the Abl kinase using peptide microarray data
J. Mol. Biol.
(2004) - et al.
Statistical analysis of protein kinase specificity determinants
FEBS Lett.
(1998) - et al.
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
J. Mol. Biol.
(1999) - et al.
Aurora kinases link chromosome segregation and cell division to cancer susceptibility
Curr. Opin. Genet. Dev.
(2004)
Mitosis: MCAK under the aura of Aurora B
Curr. Biol.
Aurora B phosphorylates centromeric MCAK and regulates its localization and microtubule depolymerization activity
Curr. Biol.
The protein kinase complement of the human genome
Science
The mouse kinome: discovery and comparative genomics of all mouse protein kinases
Proc. Natl. Acad. Sci. USA
Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
Nat. Biotechnol.
Large-scale characterization of HeLa cell nuclear phosphoproteins
Proc. Natl. Acad. Sci. USA
Phosphoproteomic fingerprinting of epidermal growth factor signaling and anticancer drug action in human tumor cells
Mol. Cancer Ther.
Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database
Plant Cell
Cited by (138)
A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction
2024, Genomics, Proteomics and BioinformaticsUsing bioinformatic resources for a systems-level understanding of phosphorylation
2024, Science BulletinElucidating the role of the L-type calcium channel in excitability and energetics in the heart: The ISHR 2020 Research Achievement Award Lecture
2022, Journal of Molecular and Cellular CardiologyPhosphorylation of RIAM by src promotes integrin activation by unmasking the PH domain of RIAM
2021, StructureCitation Excerpt :Two Src family kinases, lymphocyte-specific protein tyrosine kinase (LCK) and Fyn, are essential for T cell development and activation (Laird and Hayes, 2010; Lovatt et al., 2006; Palacios and Weiss, 2004), and have also been shown to phosphorylate RIAM in T cells (Patsoukis et al., 2009). Interestingly, RIAM possesses 20 tyrosines in total, 15 of which are located in the PH domain and the adjacent RA-PH linker and are predicted to be substrates for Src family kinases by Group-Based Prediction System (GPS), a computational prediction algorithm of cognate protein kinases (Zhou et al., 2004). Nonetheless, the regulatory role of RIAM's function in mediating integrin activity through phosphorylation in the PH domain by Src kinases remains unknown.
Prediction of Signed Protein Kinase Regulatory Circuits
2020, Cell SystemsGPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins
2020, Genomics, Proteomics and Bioinformatics
- 1
These authors contributed equally to this work.